The goal of this project, over Phases I and II, is to create a new, accurate and quantitative platform for massively parallel, ultra high throughput screening of SNPs, mutations, and gene expression on solid supports, e.g. chips. This platform, based on our novel, linear signal amplification technology, the Invader assay, will immediately impact the effort to associate SNPs and mutations with phenotypes and will be of increasing value in the molecular profiling of cancer. High throughput SNP analysis is an active area of technology development; nonetheless, most existing technologies are hampered by exclusive reliance on allele specific hybridization. The Invader assay is based on a highly specific enzyme-substrate reaction (i.e. cleavage of a precise structure formed by oligonucleotides hybridized to a target sequence). The unique accuracy of this method results from the combined specificity conferred by this sequence-specific probe hybridization and structure-specific enzymatic cleavage. This novel specificity enables direct analysis of genomic DNA or RNA, making possible simultaneous analysis of thousands of loci in a sample without intervening target amplification steps, thereby lowering costs and increasing throughput. In Phase I, we will establish the feasibility of adapting this technology to solid supports, including an initial demonstration of multiplexed analysis. PROPOSED COMMERCIAL APPLICATION: This project, over Phases I and II, could result in a low-cost, high-throughput, chip-based method for direct detection of mutations, Single Nucleotide Polymorphisms, and gene expression in a wide variety of genes. By obviating the need for costly and laborious target amplification, this simple, versatile technology the potential to replace many existing systems for routine repeat sequence-based analysis, such as array technologies and some PCR- based tests, and may contribute to the growth of the emerging molecular diagnostics market.